As i started out testing the BETA i noticed too that without propper skilling and equiptment a solo engineer doesnt stand a chance even in the mission at P'Jem with the diplomate against 2 bird of prey.
As i started over i skilled my new engineer in using weapons and overall energymanagement, that way i was able to survive most of the first encounter without sweat.
Now, that my engineer is lvl7 and i have to travel to the neutral zone i cant stand against 4 klingon battleships and 5 birds of prey as they start shoting when entering a warzone for the mission to clear off three battlezones in the sector.
Most of the time when i played i was rather alone, so there was noone in the sector who i would able to ask for help. If there are more ppl in the area its nice to team up and tear them apart. But without tier 2 ships even that is very hard and not posible without beeing killed serveral times over.